I presume that you have uninstalled and reinstalled iTunes.. I know it is simple but it often does the trick...
If not then try creating another user account on the windows machine and do that backup on there.. Do you get the same error..?

Err, Good question. The actual answer is no... As iTunes should leave them.
But I would recommend that you take a backup of them before. They should be located in C:\Documents and Settings\%username%\Application Data\Apple Computer\iTunes\Mobile Backups
Did you try creaitng another user account and try the backup with that account...

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